@article{Martini3,
abstract={The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein–protein and protein–lipid interactions and material science applications as ionic liquids and aedamers.},
author={Souza, Paulo C T and Alessandri, Riccardo and Barnoud, Jonathan and Thallmair, Sebastian and Faustino, Ignacio and Grünewald, Fabian and Patmanidis, Ilias and Abdizadeh, Haleh and Bruininks, Bart M H and Wassenaar, Tsjerk A and Kroon, Peter C and Melcr, Josef and Nieto, Vincent and Corradi, Valentina and Khan, Hanif M and Domański, Jan and Javanainen, Matti and Martinez-Seara, Hector and Reuter, Nathalie and Best, Robert B and Vattulainen, Ilpo and Monticelli, Luca and Periole, Xavier and Tieleman, D Peter and de Vries, Alex H and Marrink, Siewert J},
doi={10.1038/s41592-021-01098-3},                                             
issn={1548-7105},                                                             
journal={Nature Methods},                                                     
title={{Martini 3: a general purpose force field for coarse-grained molecular dynamics}},
url={https://doi.org/10.1038/s41592-021-01098-3},                             
year={2021}                                                                   
}
@article{Martini3smallmolecules,
  title={Martini 3 Coarse-Grained Force Field: Small Molecules},
  author={Alessandri, Riccardo and Barnoud, Jonathan and Gertsen, Anders S and Patmanidis, Ilias and de Vries, Alex H and Souza, Paulo CT and Marrink, Siewert J},
  journal={Advanced Theory and Simulations},
  volume={5},
  number={1},
  pages={2100391},
  year={2022},
  publisher={Wiley Online Library}
}
@article{MDTraj,
    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
    journal={Biophysical Journal},
    volume={109},
    number={8},
    pages={1528 -- 1532},
    year={2015},
    doi={10.1016/j.bpj.2015.08.015}
}
@article{M3_GO,
title={GōMartini 3: From large conformational changes in proteins to environmental bias corrections},
author={Souza, Paulo C. T. and Araujo, Luis P. Borges and Brasnett, Chris and Moreira, Rodrigo A. and Grunewald, Fabian and Park, Peter and Wang, Liguo and Razmazma, Hafez and Borges-Araujo, Ana C. and Cofas-Vargas, Luis F. and Monticelli, Luca and Mera-Adasme, Raul and Melo, Manuel N. and Wu, Sangwook and Marrink, Siewert J. and Poma, Adolfo B. and Thallmair, Sebastian},
url={https://www.nature.com/articles/s41467-025-58719-0},
journal={Nature Communications},
doi={10.1038/s41467-025-58719-0},
year={2025},
pages={4051},
volume={16}
}
@article{Martini3IDP,
title={Martini3-IDP: improved Martini 3 force field for disordered proteins},
author={Wang, Liguo and Brasnett, Christopher and Borges-Araújo, Luís and Souza, Paulo C. T. and Marrink, Siewert J.},
journal={Nature Communications},
volume={16},
pages={2874},
year={2025},
doi={https://doi.org/10.1038/s41467-025-58199-2}
}
